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"Captain's log: Stardate 51408.6. I've been aboard the Honshu for two days now and I still haven't spoken to him, although the doctors have assured me that he's made a full recovery. Maybe that's what I'm afraid of. Maybe I prefer to think of him as a crazy man… a broken man. He'd be less dangerous that way. As terrible as it sounds, there's a part of me that wishes he were dead. But that's a thought unworthy of a Starfleet officer. He lost an empire, he lost his daughter, and he nearly lost his mind. Whatever his crimes… isn't that enough punishment for one lifetime?"

After some small talk, Dukat engages Sisko in a discussion regarding the appearance that Sisko will be making before a special Federation Grand Jury. Sisko tries to assure Dukat by explaining that in the Federation, he is presumed innocent until proven guilty. Dukat then asks Sisko his opinion on Dukat's innocence, but Sisko ducks the question by saying that he has not read all the charges. Dukat then points out that it is not like him to equivocate. Sisko informs Dukat that he will not be tried until the end of the Dominion War and that his appearance before the special jury is just a formality. Still suspicious, Dukat reminds Sisko that he is going to be the prosecution's witness. Sisko tells him, "I'll tell them what I know."

Sisko and Dukat are shaken up in the brig of the USS Honshu

Sisko then offers his sympathies over the death of Dukat's daughter, Tora Ziyal. Still suspicious of Sisko's motives, Dukat then asks, "Do I detect the fine hand of Dr. Cox at work once again?" Sisko explains that he just wanted to offer his condolences, with Dr. Cox's permission. Dukat realizes Sisko is sincere and apologizes. Dukat explains that Dr. Cox has encouraged him to speak of Ziyal whenever possible, since it was her death that led to his momentary instability. Sisko then informs Dukat that they will reach Starbase 621 tomorrow, and he'll see him at the arraignment. As Sisko leaves, Dukat thanks Sisko, as well as MajorKira Nerys, for caring for Ziyal over the past few years. Sisko responses that it was a pleasure to have Ziyal with them and she was a wonderful young woman. Sisko then asks Dukat if he can get him anything, and Dukat jokingly asks for one bottle of Kanar and an Orionslave girl. Suddenly, the ship shakes and a red alert is sounded.

Sisko awakens and finds himself lying by a campfire in a cavern, with Dukat. Dukat tells Sisko of how they arrived on the planet in the first place – ironically, it seems that Cardassian destroyers shot them down. Sisko was heading to engineering when a plasma conduit exploded fifteen meters down the corridor from the brig, resulting in plasma burns on the left side of his body. Dukat then informs Sisko that he and LieutenantMcConnell found Sisko when the order came to abandon ship. When Sisko asks where McConnell was, Dukat reveals he died when a piece of shrapnel hit him in the head just as they were carrying Sisko into the shuttle. Sisko is told that the engines for the shuttle were damaged from the shock waves and it is grounded.

Dukat also sets up a distress beacon, which broadcasts on a neutral frequency. Sisko agrees this is fair. He finds that his broken arm is held together by an improvised cast that Dukat has made, since he does not know how to use the bone regenerator in the medkit. Dukat excuses himself to search for food, since they only have a week's worth of rations from the shuttle. "What are you planning to do with him?" inquires Weyoun, to which Dukat replies that he and Benjamin Sisko have a lot to talk about. Weyoun then reminds Dukat about the time spent in the hospital, where he had to be sedated. This recounting enrages Dukat, and he fires a phaser at Weyoun, only to leave a smoldering hole in the rock wall behind him; Weyoun is just a hallucination.

Sisko wakes up to find Dukat preparing soup. The two discuss what happened the previous night and Sisko's bout with nausea, for which he apologizes. Dukat assures him the mess was nothing compared to his days as a newly minted Glinn aboard the Kornaire, reminiscing about an incident involving three men in an compartment that had gone through an explosive decompression. Uncomfortable, Sisko tells Dukat to change the subject and in turn, Dukat sarcastically proclaims "the Emissary has spoken."

Dukat insists that Sisko should have a sense of humor about their predicament, pointing out the possibility they'll be rescued by the Dominion and commenting on how their universe can be amusing when it allows radical shifts in fortune. Sisko refuses to see any humor in their situation, but asks Dukat why he was looking around. Dukat claims it must have been the wind that he heard, offering Sisko a sip of his soup. As the two work on improving the flavor of the meal, they have another conversation regarding Deep Space 9. Dukat asks about Kira, Odo, and Quark, attempting to convince Sisko that they never gave him a chance and that his policies toward the Bajorans were actually quite generous. Dukat continues to press, claiming it was his intention to rectify the mistakes between Cardassia and Bajor. Sisko casually side-steps him by inquiring about the next ingredient for their soup.

While Dukat adds salt to the soup, he questions Sisko whether or not he'll give him the benefit of the doubt. Sisko responds with a question of his own, asking Dukat if he really does care about what he thinks. Dukat counters with another question, asking him if he cares about what his friends think of him. Sisko realizes Dukat is implying that they are friends, and makes clear that they are not friends and even though he is grateful for Dukat's saving his life, that's as friendly as they can be, and no more. Again, something catches Dukat's attention with Sisko asking him whether he's sure nothing's out there. Dukat assures him that it was the wind, but goes out to the caverns to double-check. Somewhere deeper in the caverns, Dukat now takes to arguing with a hallucination of Damar, who attempts to convince Dukat to kill Sisko now and escape to assist Cardassia in its victory. While Dukat converses with Damar, Sisko checks the transmitter and discovers that though the outside display indicates the system is online, its secondary display on the inside reveals the systems has been offline the whole time.

When Dukat returns, Sisko tells him there may be something wrong with the com system. Dukat first checks the outside display, reporting the unit to be fine. Sisko suggests that the casing should be taken off and they should run a full diagnostic just to be sure. Dukat complies and checks the inside of the transmitter but pretends to run a diagnostic, assuring Sisko that there is nothing to worry about and the unit is working. Sisko then realizes Dukat has quite intentionally been leaving it turned off.

"Ship's Log, supplemental. We have picked up a total of twelve Honshu survivors so far, but there is still no sign of Captain Sisko. We have less than twelve hours before we must abandon the search."

Alone in the cave, Sisko works on the transmitter with one of the tines he has broken off his fork. After some tinkering, Sisko manages to reset the unit's systems and bring the Distress signal back online. Hearing Dukat's approach, Sisko diligently covers up his work and hides his altered fork underneath his sheet. Dukat returns with a couple of cushions salvaged from the shuttle, shining his flashlight on Sisko, who appears to have just woken up. As Dukat helps Sisko get settled against his new cushion, the Captain comments that it appears he is planning a long stay. Dukat explains that he only wants the both of them to be comfortable as they await their rescuers.

Once Dukat settles on his own cushion, he tells Sisko about an idea that occurred to him while he was out at the shuttle. Dukat muses about how confused the Bajorans would be if they found both of them sharing the same hardships, calling himself the evil Gul Dukat, and Sisko the Emissary of the Prophets. Dukat points out that it is just the two of them, all alone, that no one is there to judge them, insisting that they both be honest with one another. He presses Sisko for his opinion on him, but is interrupted by another hallucination in the form of Kira who whispers a rather contrary opinion of her own over his shoulder.

She tells him that she thinks he is an evil, sadistic man who should have been tried as a war criminal years ago – put up against a wall and shot. This opinion prompts Dukat to question Sisko whether he agrees with Kira on how she feels about him. Sisko tells Dukat that he doesn't see any reason for discussing the matter any further. Dukat disagrees and continues, telling Sisko that his name and reputation have been slandered and twisted after the Occupation of Bajor. He states he has been wrongfully vilified throughout the Alpha Quadrant for six years and wonders out loud if Sisko is one of his detractors. Sisko insists that he cannot really pass judgment on him because he was not there during the Occupation, nor did he witness the matters with which Dukat had to struggle day after day.

The Kira hallucination warns Dukat that Sisko does not want to tell him the truth because it would upset him. Sisko watches as Dukat talks over his shoulder at the air, realizing that Dukat is delusional and hallucinating. Dukat believes that Sisko is not being entirely honest, pointing out that he's not a man who hesitates to make snap judgments when the situation calls for it. Sisko tells Dukat he is right about being judged unfairly, that he himself judged Dukat unfairly, and that he probably had good reasons for everything he did on Bajor. Dukat agrees with Sisko, and claims that some of his harsher acts were forced upon on him by Central Command.

He then explains to Sisko that he wanted to use entirely different tactics with the Bajorans, that he wished to have ruled with "a softer hand." Sisko assures Dukat that he understands, stating that he was a soldier and was only carrying out orders. Dukat eagerly agrees with this assessment only to be laughed at by Kira, who calls him a fool and tells him he is being patronized, for which Dukat yells at her. Sisko manages to return Dukat's attention to himself, suggesting that they ignore Kira and pretend she is not there. As the Defiant picks up a distress signal and beams up two additional Honshu survivors (who turn out not to be Sisko and Dukat), Dukat wildly fires his phaser at his hallucination of Kira.

Dukat later discovers Sisko's hidden fork and notices one of its missing tines, concluding after he checks the transmitter that Sisko must have repaired the unit behind his back. Outraged, Dukat destroys the transmitter, cutting the signal the Defiant picked up moments earlier, and from the debris of the transmitter he dislodges a metal bar, which he uses to attack Sisko.

Despite subspace interference over the viewscreen, Kira reminds Worf he must follow his original orders to end their search soon so they can assist the troop convoy in the Badlands. Both DoctorBashir and Miles O'Brien disagree with the Major's orders, trying to pretend they are unable to understand the message through the interference. Worf and Dax however know full well what Kira was trying to tell them, and Worf feels that ignoring the orders would be dishonorable. When Bashir openly remarks that he doesn't consider Worf's honor to be worth Captain Sisko's life, Worf dismisses him from the bridge and orders helm to lay in a course for the third planet and continue their search for the remaining time.

Sisko awakens with his head bleeding to see Dukat standing over him wiping blood from a metal pole in his grasp. Dukat tells Sisko that he brought the damage upon himself, with the groggy captain making a mention of victims that must have suffered as he has. Dukat begins to name all the things he has been called, sarcastically calling Sisko the "supreme arbiter of right and wrong in the universe." A frustrated Sisko demands what Dukat wants from him and Dukat explains that he wants no further pretenses, only their expression of their true thoughts. Sisko takes Dukat up on his challenge and begins a fierce barrage of questions – true and false, of Dukat's role in the Occupation. The murder of over five million Bajorans on his watch is Dukat's responsibility. Dukat adamantly claims otherwise, explaining that he tried to save lives during his administration. Sisko then demands evidence.

Dukat says the Occupation had already been going on for almost 40 years, but the planet was not ready for full-scale colonization. He tells Sisko that Central Command wanted the situation resolved and they didn't care how it was done. Dukat reminds Sisko that he wanted to use "a gentler hand" when dealing with the Bajorans – reducing the output quotas by fifty percent. Dukat begins to list admirable orders he gave during his tenure, for acts such as reorganizing the camps, abolishing child labor, improving medical care, and increasing food rations, for which as a result the death rate decreased by twenty percent. Dukat also explains that he had reason to punish the Bajorans as well: on his anniversary, an orbital drydock was blown up, killing over two hundred Cardassians. He explains that he then rounded up two hundred Bajoran Resistance members and executed them, claiming this retaliation was for the sake of justice rather malevolence. He goes on to mention that he also executed several more Bajorans in retaliation for a failed assassination attempt.

As Dukat continues his stories, his hallucinations of Weyoun, Damar, and Kira each support every statement in their own sardonic manner. When Dukat asks Sisko if he understands what he's saying, Sisko pretends to have been moved by his stories and posits that what happened to the Bajorans was not Dukat's fault but their own. Dukat eagerly agrees with Sisko's empty revelation as Sisko plays along, asking Dukat why the Bajorans failed to appreciate the kinder and gentler oversight he offered them. Dukat insists that the Bajorans were small-minded, ignorant fools, that the Cardassians were clearly the superior race, and they did not choose to be so – fate handed them that role.

At the height of his furious insanity, Dukat now confesses his hatred for the Bajorans and everything about them, from their religion and their Bajoran earrings to their "broken, wrinkled noses." He is most infuriated by their wishes for equality to the Cardassians. Sisko, still playing along, suggests to Dukat that maybe he should have killed them all. Dukat agrees with this assessment quite enthusiastically, proclaiming he should have "turned their planet into a graveyard the likes of which the galaxy has never seen!" Suddenly, Sisko strikes Dukat from behind with the same metal pole Dukat used on him and declares, in his most bitingly sarcastic tone, "And that is why you're NOT an evil man."

Sisko finds his way to the shuttle through a sandstorm, discovering that it is still operational. As Sisko is about to depart, however, Dukat attacks Sisko and a fight ensues. Dukat then forces Sisko out into the sandstorm while brandishing a phaser. Before Dukat departs, he thanks Sisko for their time together, promising they will not be seeing each other for awhile, and vowing "from this day forward, Bajor is dead! All of Bajor!" As the doors to the shuttle close, Dukat with his hallucinations of Weyoun, Kira, and Damar all keeping him company, smiles over an unconscious Sisko lying in the sandstorm.

It is finally time for the Defiant to leave the system in order to rendezvous with the troop convoy. As Worf orders the course set, the ship suddenly receives a hail from Gul Dukat, who lets the crew know where Captain Sisko is located.

"Ship's Log, Stardate 51413.6. We have rescued Captain Sisko, but we did not have time to locate Gul Dukat's shuttle. We are en route to our rendezvous with the troop convoy near the Badlands and the captain is recovering in sickbay."

Dax awakens Sisko, reporting that she notified Starfleet of Dukat's last known position and insisting that they'll find him. Sisko disagrees about the possibility of his capture and begins to discuss life, about how it seems complicated and that it sometimes appears everything is a shade of gray, that there is nothing truly good or evil. He then explains to Dax that after spending some time with Dukat, he has come to realize there that there is truly unambiguous evil. Dax points out that realizing the truth is one thing, but doing something about it is another. Sisko then makes clear what he is going to do about it; he makes a vow to stop Dukat from destroying Bajor.

"You and Major Kira took care of her for almost a year. I want to thank you for that; it was very generous."
"Ziyal was a very special young woman. It was a pleasure to have her with us, even if it was only a short time."
"A short time was all she ever had."

- Dukat and Sisko

"Whose signal are you transmitting? Starfleet's, or the Dominion's?"
"I'm sending out a general distress call. Whoever gets here first will find one comrade in arms, and one prisoner. That's fair, isn't it?"

- Sisko and Dukat

"The Emissary has spoken."

- Dukat

"Benjamin, just a few hours ago I was a prisoner on my way to trial and you were my dear old friend come to visit me in my cell. Now look at us. I'm free, and you're a prisoner of your own battered body and there's a good chance we'll be rescued by the Dominion. You've got to laugh at a universe that allows such radical shifts in fortune, Benjamin."
"I will laugh when a Federation starship arrives and puts you back in a cell."

- Dukat and Sisko

"You brought it on yourself, you know."
"Just like all your victims."
"All my victims. It always comes back to that, doesn't it? All my crimes. I'm such a monster, such an evil man. Behold… Benjamin Sisko: supreme arbiter of right and wrong in the universe. A man of such high moral caliber that he can sit in judgment on all the rest of us."

- Dukat and Benjamin Sisko

"What the hell do you want from me?! My approval? Is that what this is all about? You want me to give you my permission to cause more suffering and death? Well, if that's what you're after, you might as well pull out that phaser and end this right now because I will never give it to you!"
"Good!! Good; I like this. No more pretense, no games. Just you, me and the truth."
"What do you know about the truth? You bend the truth into whatever shape suits you."

- Sisko and Dukat

"The Bajorans understand a clenched fist, not an open hand."
"Being reasonable only made us bolder."
"The Dominion would've killed every man, woman and child on Bajor long ago."

- Damar, Kira, and Weyoun

"From the moment we arrived on Bajor it was clear that we were the superior race, but they couldn't accept that. They wanted to be treated as equals, when they most certainly were not. Militarily, technologically, culturally – we were almost a century ahead of them in every way. We did not choose to be the superior race. Fate handed us that role and it would have been so much easier on everyone if the Bajorans had simply accepted their role. But no… day after day they clustered in their temples and prayed for deliverance and night after night they planted bombs outside of our homes. Pride… stubborn, unyielding pride. From the servant girl that cleaned my quarters, to the condemned man toiling in a labor camp, to the terrorist skulking through the hills of Dahkur Province… they all wore their pride like some… twisted badge of honor."
"And you hated them for it."
"Of course I hated them! I hated everything about them! Their superstitions and their cries for sympathy, their treachery and their lies, their smug superiority and their stiff-necked obstinacy, their earrings, and their broken, wrinkled noses!"
"You should have killed them all, hm?"
"Yes! Yes!! That's right, isn't it?! I knew it. I've always known it. I should've killed every last one of them! I should've turned their planet into a graveyard the likes of which the galaxy had never seen! I should've killed them all."
"And that is why you're not an evil man."

- Dukat and Sisko

"I'm so glad we had this time together, Benjamin, because we won't be seeing each other for a while. I have unfinished business on Bajor. They thought I was their enemy. They don't know what it is to be my enemy, but they will. From this day forward, Bajor is dead! All of Bajor!! And this time, even their Emissary won't be able to save them!"

- Dukat

"Sometimes life seems so complicated, nothing is truly good or truly evil. Everything seems to be a shade of grey. And then you spend some time with a man like Dukat, and you realize that there is such a thing as truly evil."
"To realize that is one thing. To do something about it is another. So what are you going to do?"
"I'll tell you what I'm not going to do, I'm not going to let him destroy Bajor. I fear no evil. From now on, it's him or me."

This episode sets the stage for the showdown between Sisko and Dukat in the series finale "What You Leave Behind". Indeed, after this episode, they would not see one another again until their confrontation in the Fire Caves in the finale.

Originally, this episode was to be structured similarly to the third season episode "Distant Voices", with the regular crew appearing as different aspects of Dukat's personality. According to Ronald D. Moore, "Waltz" began life as a story we called "Dukat's Head" around the office. The notion was for Sisko to go visit Dukat in the mental hospital and while Sisko was trying to engage the catatonic Cardassian in conversation, we would push in on Dukat's face and then go inside his head and show us the fantasy life he was living. The story would've gone into the past, dealt with his Bajoran mistress, his rise to power, his treatment of the Bajorans and even the fantasy life he was trying to construct for himself on Terok Nor with Kira as his wife and himself as beloved leader of Cardassia and Bajor. We struggled with the storyline for quite a while, but never found a way to make it compelling. Eventually, we noticed that the scenes we liked the best were the ones in the hospital room between Sisko and Dukat and we decided to toss out everything but that. However, some of the character dynamics we had envisioned for the fantasy sequences eventually were realized in the phantom images of Weyoun, Damar, and Kira as they appeared in Dukat's hallucinations." (AOL chat,1998)

Of the idea behind doing the episode, Moore explains, "The intention was to dig down and reveal something in Dukat, both to the audience and to the character himself. He really did hate the Bajorans and he really does wish he'd killed them all. That's the dirty little secret he's tried not to confront head-on all these years, and now finally, he's said it out loud and accepted it about himself." (AOL chat,1998)

Ira Steven Behr echoes Moore when he says of this episode, "I wanted us to come away from this show with Dukat finally having faced who the hell he is and what he's done. To get him to finally admit that he hates the Bajorans and he wishes to kill them all. And he does. Evil may be an unclear concept in this day and age. But Dukat certainly has done evil things. And since he refuses to admit to them, we then have to simplify things, deconstruct things, until we get to the most simplistic level. Which is: 'He does evil things, therefore, he is evil'." (Star Trek: Deep Space Nine Companion)

By the time this episode aired, the character of Gul Dukat had become exceptionally popular among fans of the show, far more popular than any of the writers had ever intended. This was primarily attributed to Marc Alaimo's superbly charismatic performances as Dukat. Alaimo's portrayal had presented the audience with a character possessed of a very real pathos and sense of humor, a character with many different aspects composing his psychological make-up. The writers however were not entirely happy with how popular Dukat had become. He was supposed to be the villain of the show, and while they were proud to have created such a multi-dimensional villain, they were shocked when they saw fans online actually defending Dukat's behavior during the Occupation. Despite the writers' attempts to make Dukat the epitome of evil in subsequent shows however, his popularity would remain undiminished until the end of the series. Indeed, in relation to "Waltz", some Dukat fans were unhappy with how quickly Sisko denounces him after he tells Sisko about his initial actions as Prefect of Bajor. (Star Trek: Deep Space Nine Companion)

Of the character of Dukat, Moore comments, "Dukat is the hero of his own story. He definitely thinks that he's on the side of the angels, and he doesn't understand why everyone else doesn't see that." (Star Trek: Deep Space Nine Companion). Furthermore, he explains, "I don't see anything incompatible in the idea that Dukat wanted to be loved by those he despised. This seems to me like a complex, yet very believable, dynamic. I think you could find many, many instances where a person both loves and hates another person for very complex reasons. Dukat's egotistical need to be loved doesn't seem to be in conflict with his need to dominate and rule. In fact, one could argue that it was the Bajorans' refusal to love him (in his somewhat twisted view of reality) that prompted him to hate them." (AOL chat,1998)

This episode originally ended with Dukat saying to Sisko, "You too will learn what it's like to lose a child," but the writers abandoned this idea because it was too specific and it locked them into one path in terms of where to next take the character. They also didn't like the prospect of having to work into every single scene involving Jake that he was living his life under a death threat. (Star Trek: Deep Space Nine Companion)

Damar and Weyoun appear in this episode only as hallucinations witnessed by Dukat. Indeed, because this episode proved so popular with fans, the writers considered bringing the chorus back for the next episode involving Dukat, but they ultimately abandoned the concept as they felt the technique carried more dramatic weight by being used only once. (Star Trek: Deep Space Nine Companion)

Auberjonois also commented "Right now, I am most proud of "Waltz". If you talk to me after each episode I direct, I'll probably say to you that episode is my favorite, the best I've done, the most well-directed. But just the experience of working with Avery and Marc on "Waltz" was wonderful. It was a challenge to do what was basically a two character show. On the one hand, it was simple because I didn't have a lot of special effects with which to deal. We didn't have 100 extras, but it was a challenge too of another kind to make two people talking exciting television". ("The Shape of Things to Come", Star Trek Monthly, issue 43)

Marc Alaimo commented "That is a really terrific piece. Stories like that are usually reserved for the regulars and I was flattered that they wrote it for me. They gave me a lot of responsibility so I was glad to see that everything actually worked when it was all put together. They allow me to take a lot of chances with a character like Dukat. I get to express so many different aspects of myself in him, that I don't always get a chance to in real life. I'm very grateful that they trust me enough to write an episode like that for me. It means they like and respect my work and that makes a huge difference". (TV Zone, issue 105 & Special 44)

This episode references an attempt on Dukat's life on Terok Nor within the first month of his administration where someone placed a bomb outside his quarters. This might well be the attempt on the life of Kira Meru as seen in the episode "Wrongs Darker Than Death or Night"

When the attack on the USS Honshu begins, the officer's voice heard over the comm orders the crew to battle stations and for damage control teams to report to "level 5-J". This is an unusual statement as it is customary aboard Federation starships of this era for the various "levels" of the ship to be referred to as "Deck", followed by its numerical position within the superstructure and its comparative location amongst the other "Decks" – i.e. "Deck 5" would be located 4 levels below "Deck 1". One possible explanation for the term "5-J" could be that the officer was referring to an area within the upper pod seen on Nebula-class starships. As this pod is located upward of the bridge (usually referred to as Deck 1), alternative designations may have been assigned to the interiors of this section of the ship.

This is the second DS9 episode in a row to use a light redress of the Star Trek: Voyager brig set. It appears as the brig of the USS Honshu after appearing as a brig on a Federation starbase in the previous episode "The Magnificent Ferengi".